rs772820136
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The NM_052859.4(RFT1):c.887T>G(p.Ile296Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I296K) has been classified as Pathogenic.
Frequency
Consequence
NM_052859.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFT1 | NM_052859.4 | c.887T>G | p.Ile296Arg | missense_variant | 9/13 | ENST00000296292.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFT1 | ENST00000296292.8 | c.887T>G | p.Ile296Arg | missense_variant | 9/13 | 1 | NM_052859.4 | P1 | |
RFT1 | ENST00000394738.7 | c.770T>G | p.Ile257Arg | missense_variant | 8/12 | 5 | |||
RFT1 | ENST00000467048.1 | c.749T>G | p.Ile250Arg | missense_variant | 8/9 | 3 | |||
RFT1 | ENST00000471158.1 | n.329T>G | non_coding_transcript_exon_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
RFT1-congenital disorder of glycosylation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2009 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at